FTDI to a powered device

I'd like to add the ability to download sketches using AVRDude to a device that will be powered by a 9V battery. As it will be enclosed in a cylinder to hold both battery and ExtraCoreMD board I'd like to download code upgrades via a FTDI connection without requiring the user to disassemble and connect to a header on the ExtraCorfe.

several questions come to mind. If I miss anything important please feel free to let me know.

  1. What FTDI wires are required assuming the target device is powered on? I'm hoping to not need +5V.

  2. What would happen if the FTDI interface were connected and the target device's battery were dead?

  3. What is the absolute minimum number of wires needed? I want to keep the count down so the connector to the device will be as small as possible. I was thinking of using something like the Apple iphone headphone/microphone jack. I understand this might require some extra electronics to CTS and RTS.